Thanks Joe, That error was resolved. Now I get a different one. Please give
your suggestion.
Amin
/home/aamomin/ProteomicProcessing/TPPdownload/TPP4.8.0/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/ProteoWizard/pwiz/pwiz/data/msdata/
Serializer_MSn.cpp:263: error: expected ‘)’ before ‘const’
/home/aamomin/ProteomicProcessing/TPPdownload/TPP4.8.0/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/ProteoWizard/pwiz/pwiz/data/msdata/
Serializer_MSn.cpp:266: error: ‘Z_OK’ was not declared in this scope
/home/aamomin/ProteomicProcessing/TPPdownload/TPP4.8.0/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/ProteoWizard/pwiz/pwiz/data/msdata/
Serializer_MSn.cpp:288: error: ‘Z_OK’ was not declared in this scope
make: ***
[/home/aamomin/ProteomicProcessing/TPPdownload/TPP4.8.0/TPP-4.8.0/trans_proteomic_pipeline/src/../build/RedHatEnterpriseServer-x8
6_64/pwiz/pwiz/data/msdata/Serializer_MSn.o] Error 1
On Thursday, June 4, 2015 at 11:23:05 AM UTC-5, [email protected]
wrote:
>
> Amin,
>
> While its possible I wouldn't recommend it. From the error message it
> looks like you may be missing the bzip libraries. Make sure you have bzip
> and bzip-devel installed on your system (yum bzip-devel).
>
> -Joe
>
>
> On Thu, Jun 4, 2015 at 8:41 AM, Amin Momin <[email protected]
> <javascript:>> wrote:
>
>> Hi
>>
>> I am trying to install TPP-4.8.0 on our RHEL6.6 and I get an error due to
>> BOOST. Is there a solution for this bug. Or I just need to install Boost
>> separately.
>>
>> Thanks
>> Amin
>>
>>
>> libs/iostreams/src/bzip2.cpp:20:56: error: bzlib.h: No such file or
>> directory
>> libs/iostreams/src/bzip2.cpp:31: error: ‘BZ_OK’ was not declared in this
>> scope
>> libs/iostreams/src/bzip2.cpp:32: error: ‘BZ_RUN_OK’ was not declared in
>> this
>> sco
>>
>> pe
>> libs/iostreams/src/bzip2.cpp:33: error: ‘BZ_FLUSH_OK’ was not declared in
>> this
>> s
>>
>> cope
>> libs/iostreams/src/bzip2.cpp:34: error: ‘BZ_FINISH_OK’ was not declared
>> in
>> this
>>
>> scope
>> libs/iostreams/src/bzip2.cpp:35: error: ‘BZ_STREAM_END’ was not declared
>> in
>> this
>>
>> scope
>> libs/iostreams/src/bzip2.cpp:36: error: ‘BZ_SEQUENCE_ERROR’ was not
>> declared
>> in
>>
>> this scope
>> libs/iostreams/src/bzip2.cpp:37: error: ‘BZ_PARAM_ERROR’ was not declared
>> in
>> thi
>>
>> s scope
>> libs/iostreams/src/bzip2.cpp:38: error: ‘BZ_MEM_ERROR’ was not declared
>> in
>> this
>>
>> scope
>> libs/iostreams/src/bzip2.cpp:39: error: ‘BZ_DATA_ERROR’ was not declared
>> in
>> this
>>
>> scope
>> libs/iostreams/src/bzip2.cpp:40: error: ‘BZ_DATA_ERROR_MAGIC’ was not
>> declared
>> i
>>
>> n this scope
>> libs/iostreams/src/bzip2.cpp:41: error: ‘BZ_IO_ERROR’ was not declared in
>> this
>> s
>>
>> cope
>> libs/iostreams/src/bzip2.cpp:42: error: ‘BZ_UNEXPECTED_EOF’ was not
>> declared
>> in
>>
>> this scope
>> libs/iostreams/src/bzip2.cpp:43: error: ‘BZ_OUTBUFF_FULL’ was not
>> declared in
>> th
>>
>> is scope
>> libs/iostreams/src/bzip2.cpp:44: error: ‘BZ_CONFIG_ERROR’ was not
>> declared in
>> th
>>
>> is scope
>> libs/iostreams/src/bzip2.cpp:48: error: ‘BZ_FINISH’ was not declared in
>> this
>> sco
>>
>> pe
>> libs/iostreams/src/bzip2.cpp:49: error: ‘BZ_RUN’ was not declared in this
>> scope
>> libs/iostreams/src/bzip2.cpp: In static member function ‘static void
>> boost::iost
>>
>> reams::bzip2_error::check(int)’:
>> libs/iostreams/src/bzip2.cpp:62: error: ‘BZ_OK’ was not declared in this
>> scope
>> libs/iostreams/src/bzip2.cpp:63: error: ‘BZ_RUN_OK’ was not declared in
>> this
>> sco
>>
>> pe
>> libs/iostreams/src/bzip2.cpp:64: error: ‘BZ_FLUSH_OK’ was not declared in
>> this
>> s
>>
>> cope
>> libs/iostreams/src/bzip2.cpp:65: error: ‘BZ_FINISH_OK’ was not declared
>> in
>> this
>>
>> scope
>> libs/iostreams/src/bzip2.cpp:66: error: ‘BZ_STREAM_END’ was not declared
>> in
>> this
>>
>> scope
>> libs/iostreams/src/bzip2.cpp:68: error: ‘BZ_MEM_ERROR’ was not declared
>> in
>> this
>>
>> scope
>> libs/iostreams/src/bzip2.cpp: In constructor
>> ‘boost::iostreams::detail::bzip2_ba
>>
>> se::bzip2_base(const boost::iostreams::bzip2_params&)’:
>> libs/iostreams/src/bzip2.cpp:80: error: expected type-specifier before
>> ‘bz_strea
>>
>> m’
>> libs/iostreams/src/bzip2.cpp:80: error: expected ‘)’ before ‘bz_stream’
>> libs/iostreams/src/bzip2.cpp: In destructor
>> ‘boost::iostreams::detail::bzip2_bas
>>
>> e::~bzip2_base()’:
>> libs/iostreams/src/bzip2.cpp:83: error: expected type-specifier before
>> ‘bz_strea
>>
>> m’
>> libs/iostreams/src/bzip2.cpp:83: error: expected ‘>’ before ‘bz_stream’
>> libs/iostreams/src/bzip2.cpp:83: error: expected ‘(’ before ‘bz_stream’
>> libs/iostreams/src/bzip2.cpp:83: error: ‘bz_stream’ was not declared in
>> this
>> sco
>>
>> pe
>> libs/iostreams/src/bzip2.cpp:83: error: expected primary-expression
>> before ‘>’
>> t
>>
>> oken
>> libs/iostreams/src/bzip2.cpp:83: error: expected ‘)’ before ‘;’ token
>> libs/iostreams/src/bzip2.cpp: In member function ‘void
>> boost::iostreams::detail:
>>
>> :bzip2_base::before(const char*&, const char*, char*&, char*)’:
>> libs/iostreams/src/bzip2.cpp:88: error: ‘bz_stream’ was not declared in
>> this
>> sco
>>
>> pe
>> libs/iostreams/src/bzip2.cpp:88: error: ‘s’ was not declared in this scope
>> libs/iostreams/src/bzip2.cpp:88: error: expected type-specifier before
>> ‘bz_strea
>>
>> m’
>> libs/iostreams/src/bzip2.cpp:88: error: expected ‘>’ before ‘bz_stream’
>> libs/iostreams/src/bzip2.cpp:88: error: expected ‘(’ before ‘bz_stream’
>> libs/iostreams/src/bzip2.cpp:88: error: expected primary-expression
>> before ‘>’
>> t
>>
>> oken
>> libs/iostreams/src/bzip2.cpp:88: error: expected ‘)’ before ‘;’ token
>> libs/iostreams/src/bzip2.cpp: In member function ‘void
>> boost::iostreams::detail:
>>
>> :bzip2_base::after(const char*&, char*&)’:
>> libs/iostreams/src/bzip2.cpp:97: error: ‘bz_stream’ was not declared in
>> this
>> sco
>>
>> pe
>> libs/iostreams/src/bzip2.cpp:97: error: ‘s’ was not declared in this scope
>> libs/iostreams/src/bzip2.cpp:97: error: expected type-specifier before
>> ‘bz_strea
>>
>> m’
>> libs/iostreams/src/bzip2.cpp:97: error: expected ‘>’ before ‘bz_stream’
>> libs/iostreams/src/bzip2.cpp:97: error: expected ‘(’ before ‘bz_stream’
>> libs/iostreams/src/bzip2.cpp:97: error: expected primary-expression
>> before ‘>’
>> t
>>
>> oken
>> libs/iostreams/src/bzip2.cpp:97: error: expected ‘)’ before ‘;’ token
>> libs/iostreams/src/bzip2.cpp: In member function ‘int
>> boost::iostreams::detail::
>>
>> bzip2_base::check_end(const char*, const char*)’:
>> libs/iostreams/src/bzip2.cpp:104: error: ‘bz_stream’ was not declared in
>> this
>> sc
>>
>> ope
>> libs/iostreams/src/bzip2.cpp:104: error: ‘s’ was not declared in this
>> scope
>> libs/iostreams/src/bzip2.cpp:104: error: expected type-specifier before
>> ‘bz_stre
>>
>> am’
>> libs/iostreams/src/bzip2.cpp:104: error: expected ‘>’ before ‘bz_stream’
>> libs/iostreams/src/bzip2.cpp:104: error: expected ‘(’ before ‘bz_stream’
>> libs/iostreams/src/bzip2.cpp:104: error: expected primary-expression
>> before
>> ‘>’
>>
>> token
>> libs/iostreams/src/bzip2.cpp:104: error: expected ‘)’ before ‘;’ token
>> libs/iostreams/src/bzip2.cpp: In member function ‘void
>> boost::iostreams::detail:
>>
>> :bzip2_base::end(bool)’:
>> libs/iostreams/src/bzip2.cpp:118: error: ‘bz_stream’ was not declared in
>> this
>> sc
>>
>> ope
>> libs/iostreams/src/bzip2.cpp:118: error: ‘s’ was not declared in this
>> scope
>> libs/iostreams/src/bzip2.cpp:118: error: expected type-specifier before
>> ‘bz_stre
>>
>> am’
>> libs/iostreams/src/bzip2.cpp:118: error: expected ‘>’ before ‘bz_stream’
>> libs/iostreams/src/bzip2.cpp:118: error: expected ‘(’ before ‘bz_stream’
>> libs/iostreams/src/bzip2.cpp:118: error: expected primary-expression
>> before
>> ‘>’
>>
>> token
>> libs/iostreams/src/bzip2.cpp:118: error: expected ‘)’ before ‘;’ token
>> libs/iostreams/src/bzip2.cpp:121: error: ‘BZ2_bzCompressEnd’ was not
>> declared
>> in
>>
>> this scope
>> libs/iostreams/src/bzip2.cpp:122: error: ‘BZ2_bzDecompressEnd’ was not
>> declared
>>
>> in this scope
>> libs/iostreams/src/bzip2.cpp: In member function ‘int
>> boost::iostreams::detail::
>>
>> bzip2_base::compress(int)’:
>> libs/iostreams/src/bzip2.cpp:128: error: expected type-specifier before
>> ‘bz_stre
>>
>> am’
>> libs/iostreams/src/bzip2.cpp:128: error: expected ‘>’ before ‘bz_stream’
>> libs/iostreams/src/bzip2.cpp:128: error: expected ‘(’ before ‘bz_stream’
>> libs/iostreams/src/bzip2.cpp:128: error: ‘bz_stream’ was not declared in
>> this
>> sc
>>
>> ope
>> libs/iostreams/src/bzip2.cpp:128: error: expected primary-expression
>> before
>> ‘>’
>>
>> token
>> libs/iostreams/src/bzip2.cpp: In member function ‘int
>> boost::iostreams::detail::
>>
>> bzip2_base::decompress()’:
>> libs/iostreams/src/bzip2.cpp:133: error: expected type-specifier before
>> ‘bz_stre
>>
>> am’
>> libs/iostreams/src/bzip2.cpp:133: error: expected ‘>’ before ‘bz_stream’
>> libs/iostreams/src/bzip2.cpp:133: error: expected ‘(’ before ‘bz_stream’
>> libs/iostreams/src/bzip2.cpp:133: error: ‘bz_stream’ was not declared in
>> this
>> sc
>>
>> ope
>> libs/iostreams/src/bzip2.cpp:133: error: expected primary-expression
>> before
>> ‘>’
>>
>> token
>> libs/iostreams/src/bzip2.cpp: In member function ‘void
>> boost::iostreams::detail:
>>
>> :bzip2_base::do_init(bool, void* (*)(void*, int, int), void (*)(void*,
>> void*),
>> v
>>
>> oid*)’:
>> libs/iostreams/src/bzip2.cpp:144: error: ‘bz_stream’ was not declared in
>> this
>> sc
>>
>> ope
>> libs/iostreams/src/bzip2.cpp:144: error: ‘s’ was not declared in this
>> scope
>> libs/iostreams/src/bzip2.cpp:144: error: expected type-specifier before
>> ‘bz_stre
>>
>> am’
>> libs/iostreams/src/bzip2.cpp:144: error: expected ‘>’ before ‘bz_stream’
>> libs/iostreams/src/bzip2.cpp:144: error: expected ‘(’ before ‘bz_stream’
>> libs/iostreams/src/bzip2.cpp:144: error: expected primary-expression
>> before
>> ‘>’
>>
>> token
>> libs/iostreams/src/bzip2.cpp:144: error: expected ‘)’ before ‘;’ token
>> libs/iostreams/src/bzip2.cpp:161: error: ‘BZ2_bzCompressInit’ was not
>> declared
>> i
>>
>> n this scope
>> libs/iostreams/src/bzip2.cpp:164: error: ‘BZ2_bzDecompressInit’ was not
>> declared
>>
>> in this scope
>> ...failed updating 1 target...
>>
>> real 0m2.806s
>> user 0m4.915s
>> sys 0m0.531s
>> [ERROR] Boost libary build failed (missing
>> /home/aamomin/ProteomicProcessing/TPP
>>
>> download/TPP4.8.0/TPP-4.8.0/trans_proteomic_pipeline/src/../build/RedHatEnterpri
>>
>>
>> seServer-x86_64/boost/lib/libboost_iostreams.a), please report the results
>> of
>> ma
>>
>> nually running the following commands:
>> cd
>> /home/aamomin/ProteomicProcessing/TPPdownload/TPP4.8.0/TPP-4.8.0/trans_proteo
>>
>>
>> mic_pipeline/src/../extern/boost_1_54_0; time
>> /home/aamomin/ProteomicProcessing/
>>
>> TPPdownload/TPP4.8.0/TPP-4.8.0/trans_proteomic_pipeline/src/../extern/boost_1_54
>>
>>
>> _0/tools/build/v2/engine/bin.linuxx86_64/bjam -q -d0
>> --stagedir=/home/aamomin/Pr
>>
>> oteomicProcessing/TPPdownload/TPP4.8.0/TPP-4.8.0/trans_proteomic_pipeline/src/..
>>
>>
>> /build/RedHatEnterpriseServer-x86_64/boost
>> --build-dir=/home/aamomin/ProteomicPr
>>
>> ocessing/TPPdownload/TPP4.8.0/TPP-4.8.0/trans_proteomic_pipeline/src/../build/Re
>>
>>
>> dHatEnterpriseServer-x86_64/boost/obj --layout=system --build-type=minimal
>> -j3
>> v
>>
>> ariant=release link=static runtime-link=shared --with-filesystem
>> --with-date_tim
>>
>> e --with-iostreams --with-program_options --with-regex --with-serialization
>> --wi
>>
>> th-thread stage
>> make: *** [boost-build-libs] Error 255
>>
>>
>>
>> On Wednesday, October 16, 2013 at 4:22:51 PM UTC-5,
>> [email protected] wrote:
>>>
>>> I've identified one problem with compiling with recent versions of gcc.
>>> It has to do with a new macro TIME_UTC conflicting with a enum in boost.
>>> You can read about it here (with a workaround):
>>>
>>> https://svn.boost.org/trac/boost/ticket/6940
>>> https://bbs.archlinux.org/viewtopic.php?pid=1126374
>>>
>>> I'm working on fixing it on TPP's trunk now.
>>>
>>> -Joe
>>>
>>> --
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>>
>
>
>
> --
> Joe Slagel
> Institute for Systems Biology
> [email protected] <javascript:>
>
>
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